Open chromatin assays are known to have significant GC bias. Please take this
into consideration as necessary.
Library complexity quality metrics
Library complexity (filtered non-mito BAM)
rep1
rep2
ctl1
ctl2
Total Fragments
33221322
31305422
33803379
34022952
Distinct Fragments
28213903
24783933
32658977
33192308
Positions with Two Read
3709776
4302678
1083011
794111
NRF = Distinct/Total
0.849271
0.791682
0.966145
0.975586
PBC1 = OneRead/Distinct
0.847219
0.786039
0.96593
0.975569
PBC2 = OneRead/TwoRead
6.443341
4.527676
29.128316
40.776883
Mitochondrial reads are filtered out by default.
The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads
in a dataset; it is the ratio between the number of positions in the genome
that uniquely mapped reads map to and the total number of uniquely mappable
reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations
with EXACTLY one read pair over the genomic locations with AT LEAST one read
pair. PBC1 is the primary measure, and the PBC1 should be close to 1.
Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking,
0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is
the ratio of genomic locations with EXACTLY one read pair over the genomic
locations with EXACTLY two read pairs. The PBC2 should be significantly
greater than 1. See more details at
the ENCODE portal standard for ChIP-Seq pipeline
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'
Number of raw peaks
rep1
rep2
Number of peaks
299999
299997
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
220.0
235.0
228.0
228.0
25 percentile
880.0
940.0
486.0
910.0
50 percentile (median)
880.0
940.0
554.0
910.0
75 percentile
880.0
940.0
910.0
910.0
Max size
987.0
1149.0
1291.0
1291.0
Mean
849.3000443334811
905.8889955566223
615.8051965868246
816.2760619207421
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
15000000
15000000
Estimated Fragment Length
610
680
Cross-correlation at Estimated Fragment Length
0.150167280615788
0.13809455402583
Phantom Peak
105
105
Cross-correlation at Phantom Peak
0.1895868
0.2003833
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.1462245
0.1345435
NSC (Normalized Strand Cross-correlation coeff.)
1.026964
1.026393
RSC (Relative Strand Cross-correlation coeff.)
0.09092593
0.05393409
Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50.
Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only.
Untrimmed FASTQs are used for all the other analyses.
NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.
Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value
rep1rep2
Jensen-Shannon distance (filtered/deduped BAM)
rep1
rep2
AUC
0.27393474270597457
0.26180547357387196
Synthetic AUC
0.49329900402356563
0.4928093461905972
X-intercept
0.11277778999846019
0.12441032429913831
Synthetic X-intercept
1.1671355817523142e-190
2.267792405421769e-165
Elbow Point
0.6005403319181783
0.6059556495881518
Synthetic Elbow Point
0.5044196006278513
0.5122545607765389
JS Distance
0.1500156410880916
0.17123229799460005
Synthetic JS Distance
0.29211665188743013
0.3080898776864552
% Genome Enriched
28.623393452424995
30.280784621137737
Diff. Enrichment
23.202867473554477
25.44326296243884
CHANCE Divergence
0.19839050451514875
0.2172965290937639
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for spp raw peaks
rep1
rep2
rep1-pr1
rep2-pr1
rep1-pr2
rep2-pr2
pooled
pooled-pr1
pooled-pr2
Fraction of Reads in Peaks
0.2032381326006841
0.20804480185182508
0.21966519314813884
0.2261224449237629
0.21974182790886715
0.22613174853067985
0.19842764448416733
0.20345292468709097
0.2035529242669246
FRiP for overlap peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.11764155952963215
0.10568233193440407
0.10479529110594951
0.11822428108805347
FRiP for IDR peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.07040912655834801
0.058186155109897386
0.061869128925054064
0.06925813642709379
For spp raw peaks:
repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)
For overlap/IDR peaks:
repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates